SpaGene_LR: Identify spatially colocalized ligand-receptor pairs

In liuqivandy/SpaGene: Identify spatially localized genes and colocalized gene pairs

Identify spatially colocalized ligand-receptor pairs

Description

Identify spatially colocalized ligand-receptor pairs

Usage

SpaGene_LR(
  expr,
  location,
  normalize = T,
  topn = floor(0.2 * dim(location)[1]),
  knn = 8,
  perm = 500,
  minN = 0,
  sizefactor = 10000,
  LRpair = LRpair
)

Arguments

expr	gene expression matrix, the row is the gene and the column is the spot/cell
location	location matrix, the row number of location should match the column number of expr
normalize	whether to normalize the data (default: TRUE)
topn	the number of spots/cells considered high expression (default: 20 percent of the total spots/cells)
knn	the number of nearest neighbours to search (default: 8)
perm	the number of random permutations (default: 500)
minN	the minimum number of spots/cells with gene expression. Genes expressed equal to or less than minN spots/cells are excluded (default:0)
sizefactor	the size factor for normalization (default:10000)
LRpair	ligand-receptor pair

Value

a data frame containing the result of each ligand-receptor pair

liuqivandy/SpaGene documentation built on July 1, 2023, 6:44 a.m.